title: Effects of protein binding on a lipid bilayer containing local anesthetic articaine, and the potential of mean force calculation: a molecular dynamics simulation approach.
abstract: Articaine, as a local anesthetic drug has been simulated in neutral and charged forms, and its interaction with the dimyristoylphosphatidylcholine (DMPC) lipid bilayer membrane is investigated by molecular dynamics simulation using GROMACS software. In order to obtain the optimum location of the drug molecules, as they penetrate into the membrane, umbrella sampling is applied and the free energy is calculated. The effect of protein binding to DMPC membrane on the process of drug diffusion through the membrane is considered. Five simulation systems are designed and by applying the potential of mean force, the molecular dynamics simulation on the system is performed. In light of the obtained results, the electrostatic potential, variation of lipid bilayer's order parameter and the diffusion coefficient of drug are discussed.
authors.affiliation: Department of Chemistry, Amirkabir University of Technology, Tehran, Iran.
authors.forename: Sepideh
authors.initials: S
authors.lastname: Amjad-Iranagh
authors.forename: Abbas
authors.initials: A
authors.lastname: Yousefpour
authors.forename: Parto
authors.initials: P
authors.lastname: Haghighi
authors.forename: Hamid
authors.initials: H
authors.lastname: Modarress
mesh_terms: D000779:Anesthetics, Local / Q000737:chemistry* / Q000378:metabolism; D002355:Carticaine / Q000737:chemistry* / Q000378:metabolism; D004058:Diffusion; D004134:Dimyristoylphosphatidylcholine / Q000737:chemistry; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008051:Lipid Bilayers / Q000737:chemistry* / Q000378:metabolism; D008565:Membrane Proteins / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D055672:Static Electricity; D014867:Water / Q000737:chemistry
chemical_list: D000779:Anesthetics, Local; D008051:Lipid Bilayers; D008565:Membrane Proteins; D011506:Proteins; D014867:Water; D002355:Carticaine; D004134:Dimyristoylphosphatidylcholine